Sequence analysis of the entire RNA genome of a sweet potato chlorotic
fleck virus isolate reveals that it belongs to a distinct carlavirus species

Since the paucity of information on sweet potato
chlorotic fleck virus (SPCFV) had precluded its
classification, we have determined the complete nucleotide
sequence of the single-stranded RNA genome
of a Ugandan isolate of SPCFV. The genome is
9104 nucleotides long (excluding the poly(A) tail)
and potentially includes six open reading frames
(ORFs). Based on genomic organisation and sequence
similarity, SPCFVappears to be a member of
the genus Carlavirus (family Flexiviridae). However,
SPCFV is distantly related to typical carlaviruses,
as most of its putative gene products share amino
acid sequence identities of <40% with those of
typical carlaviruses. Its closest relative is melon
yellowing-associated virus, a proposed carlavirus
from Brazil, with which it shares ORF5 and ORF6
amino acid sequence identities of 61 and 46%,
respectively.